6-78874424-T-G

Variant names:

• chr6-78874424-T-G
• rs9352669
• NM_001010844.4:c.315+6533T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010844.4(IRAK1BP1):​c.315+6533T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,042 control chromosomes in the GnomAD database, including 17,128 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17128 hom., cov: 33)
• Consequence: IRAK1BP1 NM_001010844.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 1 publications found

Genes affected

IRAK1BP1 (HGNC:17368): (interleukin 1 receptor associated kinase 1 binding protein 1) Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRAK1BP1	NM_001010844.4	c.315+6533T>G		intron_variant	Intron 1 of 3	ENST00000369940.7	NP_001010844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRAK1BP1	ENST00000369940.7	c.315+6533T>G		intron_variant	Intron 1 of 3	1	NM_001010844.4	ENSP00000358956.1
IRAK1BP1	ENST00000606868.5	n.285+6533T>G		intron_variant	Intron 1 of 4	1		ENSP00000475570.1
IRAK1BP1	ENST00000607739.1	c.54+2289T>G		intron_variant	Intron 1 of 4	2		ENSP00000475503.1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71256 AN: 151924 Hom.: 17118 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.470

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.469 AC: 71283 AN: 152042 Hom.: 17128 Cov.: 33 AF XY: 0.473 AC XY: 35122 AN XY: 74320

African (AFR) AF: 0.384 AC: 15931 AN: 41472

American (AMR) AF: 0.458 AC: 6998 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3464

East Asian (EAS) AF: 0.695 AC: 3592 AN: 5172

South Asian (SAS) AF: 0.645 AC: 3106 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4756 AN: 10556

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33555 AN: 67972

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.477 Hom.: 2243

Bravo AF: 0.463

Asia WGS AF: 0.656 AC: 2281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.62
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9352669; hg19: chr6-79584141; COSMIC: COSV64049080;